High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Mayumi Oda, Jacob L. Glass, Reid F. Thompson, Yongkai Mo, Emmanuel N. Olivier, Maria E. Figueroa, Rebecca R. Selzer, Todd A. Richmond, Xinmin Zhang, Luke Dannenberg, Roland D. Green, Ari Melnick, Eli Hatchwell, Eric E. Bouhassira, Amit Verma, Masako Suzuki, John M. Greally

Research output: Contribution to journalArticle

107 Citations (Scopus)

Abstract

Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.

Original languageEnglish
Pages (from-to)3829-3839
Number of pages11
JournalNucleic Acids Research
Volume37
Issue number12
DOIs
Publication statusPublished - 2009
Externally publishedYes

Fingerprint

Cytosine
Methylation
Cell Count
Genetic Epigenesis
Genome
High-Throughput Nucleotide Sequencing
CpG Islands
Human Genome
Enzymes
Epigenomics
Ligation
Digestion
Polymerase Chain Reaction
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

Oda, M., Glass, J. L., Thompson, R. F., Mo, Y., Olivier, E. N., Figueroa, M. E., ... Greally, J. M. (2009). High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Research, 37(12), 3829-3839. https://doi.org/10.1093/nar/gkp260

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. / Oda, Mayumi; Glass, Jacob L.; Thompson, Reid F.; Mo, Yongkai; Olivier, Emmanuel N.; Figueroa, Maria E.; Selzer, Rebecca R.; Richmond, Todd A.; Zhang, Xinmin; Dannenberg, Luke; Green, Roland D.; Melnick, Ari; Hatchwell, Eli; Bouhassira, Eric E.; Verma, Amit; Suzuki, Masako; Greally, John M.

In: Nucleic Acids Research, Vol. 37, No. 12, 2009, p. 3829-3839.

Research output: Contribution to journalArticle

Oda, M, Glass, JL, Thompson, RF, Mo, Y, Olivier, EN, Figueroa, ME, Selzer, RR, Richmond, TA, Zhang, X, Dannenberg, L, Green, RD, Melnick, A, Hatchwell, E, Bouhassira, EE, Verma, A, Suzuki, M & Greally, JM 2009, 'High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers', Nucleic Acids Research, vol. 37, no. 12, pp. 3829-3839. https://doi.org/10.1093/nar/gkp260
Oda, Mayumi ; Glass, Jacob L. ; Thompson, Reid F. ; Mo, Yongkai ; Olivier, Emmanuel N. ; Figueroa, Maria E. ; Selzer, Rebecca R. ; Richmond, Todd A. ; Zhang, Xinmin ; Dannenberg, Luke ; Green, Roland D. ; Melnick, Ari ; Hatchwell, Eli ; Bouhassira, Eric E. ; Verma, Amit ; Suzuki, Masako ; Greally, John M. / High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. In: Nucleic Acids Research. 2009 ; Vol. 37, No. 12. pp. 3829-3839.
@article{05a4ee9677914497a8ed5078c24e2590,
title = "High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers",
abstract = "Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5{\%} of CpG islands and 91.1{\%} of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.",
author = "Mayumi Oda and Glass, {Jacob L.} and Thompson, {Reid F.} and Yongkai Mo and Olivier, {Emmanuel N.} and Figueroa, {Maria E.} and Selzer, {Rebecca R.} and Richmond, {Todd A.} and Xinmin Zhang and Luke Dannenberg and Green, {Roland D.} and Ari Melnick and Eli Hatchwell and Bouhassira, {Eric E.} and Amit Verma and Masako Suzuki and Greally, {John M.}",
year = "2009",
doi = "10.1093/nar/gkp260",
language = "English",
volume = "37",
pages = "3829--3839",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "12",

}

TY - JOUR

T1 - High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

AU - Oda, Mayumi

AU - Glass, Jacob L.

AU - Thompson, Reid F.

AU - Mo, Yongkai

AU - Olivier, Emmanuel N.

AU - Figueroa, Maria E.

AU - Selzer, Rebecca R.

AU - Richmond, Todd A.

AU - Zhang, Xinmin

AU - Dannenberg, Luke

AU - Green, Roland D.

AU - Melnick, Ari

AU - Hatchwell, Eli

AU - Bouhassira, Eric E.

AU - Verma, Amit

AU - Suzuki, Masako

AU - Greally, John M.

PY - 2009

Y1 - 2009

N2 - Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.

AB - Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.

UR - http://www.scopus.com/inward/record.url?scp=67651149735&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67651149735&partnerID=8YFLogxK

U2 - 10.1093/nar/gkp260

DO - 10.1093/nar/gkp260

M3 - Article

C2 - 19386619

AN - SCOPUS:67651149735

VL - 37

SP - 3829

EP - 3839

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 12

ER -